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PDBsum entry 1zvq
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References listed in PDB file
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Key reference
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Title
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Structure of a transient intermediate for gtp hydrolysis by ras.
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Authors
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B.Ford,
V.Hornak,
H.Kleinman,
N.Nassar.
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Ref.
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Structure, 2006,
14,
427-436.
[DOI no: ]
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PubMed id
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Abstract
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The flexibility of the conserved 57DTAGQ61 motif is essential for Ras proper
cycling in response to growth factors. Here, we increase the flexibility of the
57DTAGQ61 motif by mutating Gln61 to Gly. The crystal structure of the RasQ61G
mutant reveals a new conformation of switch 2 that bears remarkable structural
homology to an intermediate for GTP hydrolysis revealed by targeted molecular
dynamics simulations. The mutation increased retention of GTP and inhibited Ras
binding to the catalytic site, but not to the distal site of Sos. Most
importantly, the thermodynamics of RafRBD binding to Ras are altered even though
the structure of switch 1 is not affected by the mutation. Our results suggest
that interplay and transmission of structural information between the switch
regions are important factors for Ras function. They propose that initiation of
GTP hydrolysis sets off the separation of the Ras/effector complex even before
the GDP conformation is reached.
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Figure 2.
Figure 2. Comparison of the Switch Regions of RasQ61G with
WT-Ras and RasA59G
(A) Superposition of the switch 1 (Sw 1)
and switch 2 (Sw 2) regions of the GppNp bound forms of WT-Ras
(yellow) (Pai et al., 1990) and RasQ61G (blue). The GppNp and
Mg^2+ ions are in ball-and-stick representation in purple and
green, respectively. The water molecule in WT-Ras responsible
for the nucleophilic attack on the γ-phosphate (W175) is shown
as a yellow sphere; the closest water molecule in the RasQ61G
structure is shown as a blue sphere.
(B) Superposition of
the switch regions of the GppNp bound forms of RasA59G (gold)
(Hall et al., 2002) and RasQ61G (blue). Dotted lines represent
hydrogen bonds. For simplicity, only a few residues in each
region are shown.
This figure was prepared with Molscript
(Kraulis, 1991) and Pymol (http://pymol.sourceforge.net/).
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Figure 6.
Figure 6. Evolution of the Switch Regions along the Path for
GTP Hydrolysis
(A–D) Backbone atoms of both switch 1
(pink, residues 25–40) and switch 2 (yellow, residues 57–75)
are shown along with key side chain residues for simplicity. The
guanine nucleotide (GTP/GDP) and the Mg^2+ ion are shown in a
ball-and-stick model. (A) The beginning of the path (Ras•GTP)
(Pai et al., 1990). (B) Transient intermediate 1 (RasQ61G). (C)
Transient intermediate 2 (RasA59G) (Hall et al., 2002). (D) The
end of the path (Ras•GDP) (Milburn et al., 1990). Hydrogen
bonds between switch regions and other key hydrogen bonds are
denoted by dotted lines.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(2006,
14,
427-436)
copyright 2006.
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Secondary reference #1
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Title
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The structural basis for the transition from ras-Gtp to ras-Gdp.
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Authors
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B.E.Hall,
D.Bar-Sagi,
N.Nassar.
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Ref.
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Proc Natl Acad Sci U S A, 2002,
99,
12138-12142.
[DOI no: ]
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PubMed id
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Figure 1.
Fig 1. Structural changes induced in Ras switch regions by
the glycine for alanine substitution at position 59. Close-up
view of Glu-37 (switch 1) and Arg-68 (switch 2) in the crystal
structures of wild-type Ras (A) (15) and RasA59G (B) in the
GppNp-bound forms. Switch 1 (SwI) and switch 2 (SwII) are in
magenta and yellow, respectively. Loop L4 and helix-  2 of
switch 2 are labeled. The GppNp and the Mg2+-ion are in light
blue, and water molecules (W) are represented by red spheres.
Tyr-32 is in pink, Glu-37 in red, and Arg-68 in blue. Hydrogen
bonds are represented by dashed lines and the van der Waals
interactions between Glu-37 and Tyr-71 (B) are indicated by a
dotted line. In wild-type Ras (A), Arg-68 stabilizes the N
terminus of the switch 2 region (60-62) through direct or
water-mediated hydrogen bonds. In RasA59G (B), Glu-37 makes
hydrogen bonds with Arg-68 and van der Waals interactions with
Tyr-71, which protects it partially from the solvent. Tyr-64,
which is essential for Sos-binding by Ras, adopts a position
that inhibits the docking of the two proteins. The catalytic
residue Gln-61 is positioned far from W175. Tyr-32 is making a
water-mediated hydrogen bond with the  -phosphate, and its bulky
phenol group is protecting the phosphates from the surrounding
solvent. (C) Stereo representation of the superposition of the C
of
switch 1 and 2 regions between the structures of wild-type Ras
(green) and RasA59G (gold) in the GppNp-bound form. The residues
of L4 are shown, whereas only the side chains of Tyr-32, Glu-37,
Gln-61, Arg-68, and Tyr-71 are shown. The two water molecules
(W332 and W349) in wild-type Ras that coordinated Arg-68 and
that have been exchanged with the solvent on the reorientation
of the switch 2 region, are shown. Prepared with MOLSCRIPT (24)
and RASTER3D (25).
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Figure 2.
Fig 2. Structural changes that affect the switch 1 and
switch 2 regions of Ras along the path for GTP hydrolysis.
Structures proceed from the GTP-bound form (Left, PDB
coordinates 5P21 [PDB]
), to the intermediate (Center) that is represented by the A59G
mutant, and finally to the GDP-bound form (Right, PDB
coordinates 4Q21). Water molecules are shown as red spheres; the
nucleotide and the Mg2+-ion are in light blue. Switch 1 is in
magenta and switch 2 in gold. Close contacts are represented by
dotted lines.
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